Research Assistant I - van Opijnen and Rakoff-Nahoum labs

Position Summary:
The van Opijnen and Rakoff-Nahoum labs are seeking a Research Assistant for a minimum of 2 years.

The position is ideal for postbacs applying to graduate/medical school in the near future. The position would involve molecular biology, DNA/RNA extraction/purification, library prep and next generation sequencing for bacterial genomics, metagenomics, bacterial and host RNASeq, metatranscriptomics and single cell RNASeq

The goal of the Rakoff-Nahoum lab is a comprehensive understanding of the host-associated microbiota at various levels of biological organization: from genes to molecules to organisms to ecosystems, and importantly, the determination of cause and effect. To achieve this, we couple empirical approaches with ecological and evolutionary frameworks. We use the tools of classic bacterial genetics of gut anaerobes including the cultivation, random and directed mutagenesis of individual members of the mammalian microbiota (Bacteroidetes, Firmicutes, Actinobacteria), in vitro and in vivo experimental systems to study the adaptation of gut bacteria to the environment (such as using TnSeq), mouse gnotobiotics, computational approaches to microbiome ecology, and high throughput in vitro pipelines for the cultivation, genetic, chemical and phenotypic analysis of the effects of members of the microbiota on each other and the host.

The van Opijnen lab Experimental & Computational Tool Development focuses on capturing how an entire pathogen responds to and interacts with its environment, such as the host and or drugs. Thereby, when we develop a new tool we always consider how to capture as much of the organism as possible. For instance, a simple example is to capture a pathogen's entire transcriptome in response to a specific environment, or how all the genes in the genome contribute to a specific phenotype. A second consideration is how to make the tool high throughput, for instance, instead of measuring one response to one condition or drug, how can we measure how these responses change over time, and in response to hundreds of conditions? Consequently, and this is a key point, such approaches generate large amounts of data, which require appropriate tools to assist in processing and analysis. This creates opportunities to develop machine learning/AI-mediated approaches to uncover non-obvious patterns in the data that not only reveal new biological insights, but can be leveraged to design novel treatment strategies. Examples of experimental and computational tools are: Tn-Seq and Hii-TnSeq: Advanced techniques for genome-wide mapping of bacterial responses to environmental stresses and host immune factors, highlighting genetic determinants of drug sensitivity and immune evasion. Droplet Tn-Seq: A microfluidic approach enabling the analysis of thousands of single bacterial cells simultaneously, unlocking insights into cell-to-cell communication and antibiotic interactions. CRISPRi-TnSeq and dualCRISPRI: CRISPR interference, possibly combined with Tn-Seq to create detailed genetic interaction networks, expanding our understanding of a genome-wide bacterial architecture.

Key Responsibilities:

• Performs a variety of routine laboratory experiments and procedures, utilizing standard laboratory equipment, recording and checking results for completeness and accuracy
• Assists in troubleshooting procedures if experimental results are unexpected or quality of specimens is poor
• Performs the following techniques typically required for the lab:
  • Maintains records of results and methodologies in a log of work performed
  • Maintains equipment, lab area, and supplies in a neat professional manner
  • Sterilize and clean glassware, and prepare media and other materials using appropriate procedures
  • Inventories supplies, alerts supervisor to needed supplies, or mixes standard reagents
  • Processes orders for supplies

Minimum Qualifications
Education:

• A Bachelor's degree is required